"The younger Michael Flynn was helping his father with some administration and scheduling duties early on in the transition process," Trump team spokesman Jason Miller said, adding that Michael Flynn Jr. is "no longer involved with the transition efforts."
"Until #Pizzagate proven to be false, it'll remain a story. The left seems to forget #PodestaEmails and the many "coincidences" tied to it," Flynn Jr. said in one of his tweets.
Welch, 28, allegedly drove to Washington from Salisbury, North Carolina, to investigate "Pizzagate" and fired one shot from an assault rifle inside the restaurant, sending patrons fleeing. There were no reports of injuries.
D.C. police called the Comet Ping Pong story "a fictitious online conspiracy theory" in a statement and charged Welch with assault.
It was unclear whether Welch has entered a plea.
Michael Flynn Sr. has also used his social media as a platform to promote fake news stories involving Clinton. He has not commented on his tweets.